Contacts of the helix formed by residues 169 - 178 (chain B) in PDB entry 4DBW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B ASN 4.0 0.6 + - - -
168B PHE* 1.3 75.1 - - - +
170B ARG* 1.3 66.2 + - - +
171B ARG* 3.2 29.1 + - - +
172B GLN* 2.8 43.3 + - - +
173B LEU* 2.9 22.6 + - - +
199B ARG* 5.7 4.0 - - - +
202B LEU* 4.4 3.6 - - - -
317B TYR 4.4 1.6 + - - -
318B PRO* 3.0 37.0 + - + +
321B ASP* 3.7 9.8 + - - -
323B TYR* 3.7 15.9 - - - +
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Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 6.1 3.2 - - - +
169B ASN* 1.3 71.2 - - - +
171B ARG* 1.3 59.6 + - - +
173B LEU* 3.2 8.7 + - - +
174B GLU* 2.8 57.5 + - + +
202B LEU* 4.0 8.7 - - + +
205B PHE* 3.8 34.1 - - + -
322B GLU 5.7 0.4 - - - -
323B TYR* 2.9 65.9 + - + +
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Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASN* 3.2 20.5 + - - +
170B ARG* 1.3 81.7 - - - +
172B GLN* 1.3 69.6 + - - +
174B GLU* 3.3 11.4 - - + +
175B MET* 3.1 55.2 + - + +
315B PRO 4.1 17.4 + - - -
316B ASN* 5.1 2.8 + - - -
317B TYR 5.1 4.8 + - - -
320B SER* 5.5 1.6 - - - -
321B ASP* 2.5 53.5 + - - +
323B TYR* 5.0 0.4 + - - -
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Residues in contact with GLN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B PRO* 3.6 20.0 - - + +
144B LEU* 5.3 2.9 - - + +
168B PHE* 3.5 26.9 - - + -
169B ASN* 2.8 44.7 + - - +
171B ARG* 1.3 85.9 - - - +
173B LEU* 1.3 67.7 + - - +
175B MET* 3.4 31.1 + - + +
176B ILE* 3.5 12.3 + - - +
316B ASN* 2.9 43.8 + - - +
318B PRO* 3.9 5.2 - - - +
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B VAL* 3.7 19.1 - - + -
168B PHE* 3.4 29.8 - - + -
169B ASN 2.9 13.6 + - - +
170B ARG 3.4 7.0 - - - +
172B GLN* 1.3 75.6 - - - +
174B GLU* 1.3 58.9 + - - +
176B ILE* 3.0 9.2 + - + +
177B LEU* 2.8 33.9 + - + +
186B PRO* 5.4 5.4 - - + -
189B ASN* 3.6 24.5 - - + +
202B LEU* 3.9 18.8 - - + -
205B PHE* 3.8 22.4 - - + -
206B CYS* 4.1 9.6 - - - -
211B ILE* 4.4 15.9 - - + -
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Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ARG* 2.8 50.0 + - + +
171B ARG* 3.3 12.8 - - - +
173B LEU* 1.3 76.5 - - - +
175B MET* 1.3 53.7 + - - +
177B LEU* 3.8 11.6 - - - +
178B ASN* 2.7 60.5 + - - +
205B PHE* 3.5 24.2 - - + -
209B LYS* 4.0 12.3 + - - -
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Residues in contact with MET 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B LEU* 6.2 7.9 - - + -
145B CYS* 3.6 20.8 - - - -
171B ARG* 3.1 51.4 + - + +
172B GLN* 3.4 20.9 - - + +
173B LEU 3.2 0.2 - - - -
174B GLU* 1.3 76.9 - - - +
176B ILE* 1.3 64.6 + - + +
178B ASN* 3.9 2.3 - - - +
179B LYS* 3.3 14.2 + - - -
316B ASN* 5.8 5.2 - - - +
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Residues in contact with ILE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 6.0 1.1 - - + -
144B LEU* 3.9 31.2 - - + +
145B CYS* 4.2 11.4 - - - -
148B TRP* 3.7 43.5 - - + +
165B VAL* 5.2 3.4 - - + -
168B PHE* 4.3 15.7 - - + -
172B GLN 3.5 14.4 - - - +
173B LEU* 3.0 8.1 + - - +
175B MET* 1.3 77.3 - - + +
177B LEU* 1.3 67.9 + - - +
179B LYS* 3.0 22.5 + - + +
182B LEU* 3.3 9.7 - - + +
186B PRO* 4.0 23.6 - - + -
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU* 6.0 0.4 - - - +
173B LEU* 2.8 25.5 + - + +
174B GLU* 3.6 20.2 - - - +
176B ILE* 1.3 72.2 - - - +
178B ASN* 1.3 63.2 + - - +
179B LYS 3.3 1.3 - - - +
182B LEU* 3.3 18.4 - - - +
185B LYS* 3.9 32.5 - - + -
186B PRO* 4.1 11.7 - - + -
205B PHE* 4.0 10.5 - - + -
209B LYS* 3.8 37.7 - - + +
211B ILE* 4.0 19.5 - - + -
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Residues in contact with ASN 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LYS* 5.7 4.7 + - - -
174B GLU* 2.7 49.3 + - - +
175B MET* 3.9 3.6 - - - +
177B LEU* 1.3 75.9 - - - +
179B LYS* 1.3 66.0 + - - +
180B PRO* 3.4 6.9 - - - +
209B LYS* 5.6 2.1 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il